X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 18% (v/v) PEG 5000 MME, 100mM Bis-Tris, 200mM sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 169.89 α = 90
b = 69.76 β = 96.34
c = 48.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9642 PHOTON FACTORY BL-17A

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 47.84 99.2 0.074 0.074 -- 3.6 37892 37589 0.0 0.0 18.85
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.11 98.7 0.407 0.407 3.1 3.6 5444

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.0 43.804 -- 1.35 37900 37582 1882 99.16 0.2139 0.2139 0.212 0.2486 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.0 2.0541 -- 144 2707 0.2495 0.3057 -- 99.0
X Ray Diffraction 2.0541 2.1145 -- 140 2736 0.2273 0.2893 -- 99.0
X Ray Diffraction 2.1145 2.1828 -- 137 2725 0.2221 0.2637 -- 99.0
X Ray Diffraction 2.1828 2.2608 -- 145 2695 0.2166 0.2821 -- 99.0
X Ray Diffraction 2.2608 2.3513 -- 149 2738 0.2164 0.2687 -- 99.0
X Ray Diffraction 2.3513 2.4583 -- 135 2724 0.2341 0.305 -- 99.0
X Ray Diffraction 2.4583 2.5879 -- 147 2764 0.2307 0.2928 -- 99.0
X Ray Diffraction 2.5879 2.75 -- 128 2764 0.2355 0.2567 -- 100.0
X Ray Diffraction 2.75 2.9623 -- 150 2747 0.2311 0.2816 -- 100.0
X Ray Diffraction 2.9623 3.2603 -- 144 2780 0.22 0.2619 -- 100.0
X Ray Diffraction 3.2603 3.7319 -- 169 2748 0.2052 0.239 -- 100.0
X Ray Diffraction 3.7319 4.7009 -- 131 2802 0.1779 0.2047 -- 100.0
X Ray Diffraction 4.7009 43.8146 -- 163 2770 0.2092 0.2231 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.5243
Anisotropic B[1][1] -5.2402
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.7172
Anisotropic B[2][2] -0.6102
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.8504
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.048
f_dihedral_angle_d 10.792
f_angle_d 0.672
f_bond_d 0.003
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2664
Nucleic Acid Atoms 1050
Heterogen Atoms 0
Solvent Atoms 310

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
ADSC version: Quantum data collection